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CaTISSUE Suite Nov. 2007

CaTISSUE Suite Nov. 2007. Rakesh Nagarajan, M.D., Ph.D. Mark A. Watson, M.D., Ph.D. Washington Univ. / Siteman Cancer Center. Srikanth Adiga Kapil Kaveeshwar Poornima Govindrao Aarti Sharma Gautam Shetty Mandar Deshmukh. caTISSUE. 050107. Suite. http://caBIG.nci.nih.gov.

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CaTISSUE Suite Nov. 2007

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  1. CaTISSUE Suite Nov. 2007 Rakesh Nagarajan, M.D., Ph.D. Mark A. Watson, M.D., Ph.D. Washington Univ. / Siteman Cancer Center Srikanth Adiga Kapil Kaveeshwar Poornima Govindrao Aarti Sharma Gautam Shetty Mandar Deshmukh caTISSUE 050107 Suite http://caBIG.nci.nih.gov

  2. caTISSUE Core 1.1 (WU) – Core object model and reference inventory system for research biospecimen management. • caTISSUE Clinical Annotation Engine 1.2 (UPMC) - Annotation of biospecimens with pathology data using CAP protocol data elements. Tissue Banks and Pathology Tools (December 2006) caTIES 2.0 (UPMC) - Text extraction and de-identification of surgical pathology reports. Query and request system for archived tissue blocks.

  3. caTISSUE Suite Requested Features (Discussion / Prioritization- July 2006) • Resolution of caTISSUE Core bugs based upon ‘real life’ utilization • Improved usability and workflow of caTISSUE Core based upon ‘real life’ utilization • Integration of caTIES and caTISSUE Core • UML modeling • Updating HL7 data loader with matching algorithms and new model support • User interface to view pathology reports along with associated biospecimen data objects

  4. caTISSUE Suite Requested Features (Discussion / Prioritization- July 2006) • Integration of caTISSUE CAE and caTISSUE Core • UML modeling of CAP protocol CDEs to backbone objects • Less detailed but more comprehensive pathology representation • Clinical data: • Environmental exposure (Smoking, Alcohol) • Family history • Clinical events / follow-up • Therapy • Dynamic data extensions • User interface to add data elements • Query based on local data elements

  5. caTISSUE Suite Requested Features (Discussion / Prioritization- July 2006) • Informed consent tracking • Biospecimen request and fulfillment • Based on pathology report cases (caTIES) • Biospecimens • Biospecimen derivatives • Biospecimen arrays • Integrated query interface • Support queries across biospecimens, reports, annotation, and data extensions. • Query across multiple instances of caTissue • Temporal query • New query interface • Ability to store queries & results • Ability to join query results

  6. caTISSUE Suite Dynamic Extensions • Create new classes (entities) dynamically and associate them with the caTISSUE Core static model • Class, attribute, and associated metadata - Add/Edit/Delete • Data entry form generation: Form view and spreadsheet view • Validation rules (UI as well as backend) • Permissible values support (custom, EVS, CDE) • Security for identified attributes • Entity reuse - Copy & share attributes • XMI: Import and export • caCORE API to add, edit and read

  7. Metadata structure MODEL EVS 1..* CLASS 1..* Concept Code 1..* ATTRIBUTES Download value domain Class reuse 1..* PERMISSIBLE VALUES CDE reuse caDSR

  8. Administrator creates new custom annotations System stores metadata and creates RDBMS tables to store actual data CREATE Technician wants to add custom annotation System auto generates web page to add custom annotation System adds data to the database DATA Researcher query for Specimens based on custom annotation System auto generates query criteria pages and provides ability to query across static and dynamic model QUERY Dynamic extension use cases

  9. Sample entity creation user interface Build a Form 1. Define Form 2. Build Entity 3. Preview Case Add new attribute Current Attributes Text Field Name Text Field CDE: Label : Datatype Size: Default Value: Permissible values: Check Box Get info from caDSR ID Text Field Radio Button Disease Check Box Type List List Tissue File Upload Hierarchical Tree Add Grid URL Add associated class Save & Add Down Up Delete Previous Next

  10. Consent Tracking Requirements for caTISSUE Suite • July 19, 2006 End users meet to discuss requirements for caTISSUE Suite. Consent tracking given high priority. Consent tracking working group formed. (MD Anderson, PENN, UPMC, Dartmouth, Duke, TJU, NCI) • August 2006 Consent tracking working group identified key requirements for consent tracking functionality. • Sept. 2006 Summary document of consent tracking requirements created and reviewed by DSIC (see CVS). • Oct. 2006 Formal software requirements and wire frames for UI created by caTISSUE Suite development team (see CVS). • Dec. 2006 First iteration prototype of caTISSUE Suite application with consent tracking.

  11. caTISSUE Suite Consent Tracking Model

  12. Help

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  24. Biospecimen Request Fulfillment in caTISSUE Suite 1. Specimen Query Result

  25. 2. Generate Request List

  26. 3. Create Order Based on Distribution Protocol

  27. 4. Request a biospecimen from the list

  28. 5. Request a derivative from a biospecimen on the list

  29. 6. Request a tissue block from an SPR case

  30. 7. Review of pending requests

  31. 8. Review specimen status for request

  32. caTISSUE Iterative Development Plan Milestone 1 (Dec. 15, 2006) • Harmonized UML model (in progress) • Dynamic extensions – simple object creation (in progress) • Design of query Interface (in progress) • Documentation (done) Milestone 2 (Jan 2007) • HL7 path data loader (in progress) • Distribution (in progress) • Consent tracking (SRS done) • Updates to UML model • Dynamic extensions – complex object creation • Query Interface • Finalize usability enhancements • Incorporate adopter comments • Documentation • APIs

  33. caTISSUE Iterative Development Plan Milestone 3 (Feb. 2007) • DE-ID pipeline changes (in progress) • Dynamic extensions – Support for permissible values • Integrated query Interface • Implement usability enhancements • Incorporate adopter comments • Documentation • API Milestone 4 (March 2007) • Concept coding pipeline changes • Dynamic extensions • Integrated query interface • Implement usability enhancements • Incorporate adopter comments • Documentation • Installer • API

  34. caTISSUE Iterative Development Plan • Milestone 5 (April 2007) • Installer • Integrated query interface • Bug fixing and testing • Documentation • API • Milestone 6 (May 2007) • Bug fixing and testing • Documentation • API

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